Error in UseMethod("filter_") : no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"
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Entering edit mode
antara • 0
@antara-24297
Last seen 9 months ago

I am trying to run honeyBADGER and when I run code similar to this

hb$setGexpMats(gexp, ref, mart.obj, filter=FALSE, scale=FALSE, verbose=TRUE)


I get following error

Error in UseMethod("filter_") : 
  no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"


traceback()
19: filter_(., ~rid == NA_character_)
18: function_list[[k]](value)
17: withVisible(function_list[[k]](value))
16: freduce(value, `_function_list`)
15: `_fseq`(`_lhs`)
14: eval(quote(`_fseq`(`_lhs`)), env, env)
13: eval(quote(`_fseq`(`_lhs`)), env, env)
12: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
11: tbl %>% filter_(~rid == NA_character_)
10: tryCatchList(expr, classes, parentenv, handlers)
9: tryCatch({
       con <- .sql_connect_RO(.sql_dbfile(bfc))
       src <- src_dbi(con)
       tbl <- tbl(src, "resource")
       if (missing(rids)) {
       }
       else if (length(rids) == 0) {
           tbl <- tbl %>% filter_(~rid == NA_character_)
       }
       else if (length(rids) == 1) {
           tbl <- tbl %>% filter_(~rid == rids)
       }
       else {
           tbl <- tbl %>% filter_(~rid %in% rids)
       }
       meta <- setdiff(dbListTables(con), .RESERVED$TABLES)
       for (m in meta) tbl <- left_join(tbl, tbl(src, m), by = "rid")
       tbl <- tbl %>% collect
   }, finally = {
       dbDisconnect(con)
   })
8: .sql_get_resource_table(x, rids)
7: bfcinfo(x, rids)
6: bfcinfo(x, rids)
5: bfcquery(bfc, query = hash, field = "rname")
4: bfcquery(bfc, query = hash, field = "rname")
3: .checkCache(bfc, hash)
2: getBM(values = rownames(gexp.norm), attributes = c(id, "chromosome_name", 
       "start_position", "end_position"), filters = c(id), mart = mart.obj)
1: lt$setGexpMats(temp.ltgexp, lagexp.m, mart.obj, filter = FALSE, 
       scale = FALSE, verbose = TRUE)

sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.1

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] EnsDb.Hsapiens.v79_2.99.0              
 [2] ensembldb_2.10.2                       
 [3] AnnotationFilter_1.10.0                
 [4] forcats_0.5.0                          
 [5] stringr_1.4.0                          
 [6] purrr_0.3.4                            
 [7] readr_1.4.0                            
 [8] tidyr_1.1.2                            
 [9] tibble_3.0.4                           
[10] ggplot2_3.3.2   
[11] tidyverse_1.3.0                        
[12] dplyr_1.0.2                            
[13] randomForest_4.6-14                    
[14] data.table_1.13.2                      
[15] BSgenome.Hsapiens.UCSC.hg19_1.4.0      
[16] BSgenome_1.54.0                        
[17] Biostrings_2.54.0                      
[18] XVector_0.26.0                         
[19] org.Hs.eg.db_3.10.0                    
[20] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[21] GenomicFeatures_1.38.2                 
[22] AnnotationDbi_1.48.0                   
[23] Biobase_2.46.0                         
[24] AnnotationHub_2.18.0                   
[25] BiocFileCache_1.10.2                   
[26] dbplyr_2.0.0                           
[27] rtracklayer_1.46.0                     
[28] GenomicRanges_1.38.0                   
[29] GenomeInfoDb_1.22.1                    
[30] IRanges_2.20.2                         
[31] S4Vectors_0.24.4                       
[32] BiocGenerics_0.32.0                    
[33] biomaRt_2.42.1                         
[34] HoneyBADGER_0.1                        
[35] rjags_4-10                             
[36] coda_0.19-4                            

loaded via a namespace (and not attached):
 [1] colorspace_2.0-0              ellipsis_0.3.1               
 [3] rprojroot_2.0.2               fs_1.5.0                     
 [5] rstudioapi_0.13               remotes_2.2.0                
 [7] bit64_4.0.5                   fansi_0.4.1                  
 [9] interactiveDisplayBase_1.24.0 lubridate_1.7.9.2            
[11] xml2_1.3.2                    pkgload_1.1.0                
[13] jsonlite_1.7.1                Rsamtools_2.2.3              
[15] broom_0.7.2                   shiny_1.5.0                  
[17] BiocManager_1.30.10           compiler_3.6.2               
[19] httr_1.4.2                    backports_1.2.0              
[21] assertthat_0.2.1              Matrix_1.2-18                
[23] fastmap_1.0.1                 lazyeval_0.2.2               
[25] cli_2.2.0                     later_1.1.0.1                
[27] htmltools_0.5.0               prettyunits_1.1.1            
[29] tools_3.6.2                   gtable_0.3.0                 
[31] glue_1.4.2                    GenomeInfoDbData_1.2.2       
[33] reshape2_1.4.4                rappdirs_0.3.1               
[35] Rcpp_1.0.5                    cellranger_1.1.0             
[37] vctrs_0.3.5                   ps_1.4.0                     
[39] testthat_3.0.0                rvest_0.3.6                  
[41] mime_0.9                      lifecycle_0.2.0              
[43] devtools_2.3.2                XML_3.99-0.3                 
[45] zlibbioc_1.32.0               scales_1.1.1                 
[47] hms_0.5.3                     promises_1.1.1               
[49] ProtGenerics_1.18.0           SummarizedExperiment_1.16.1  
[51] yaml_2.2.1                    curl_4.3                     
[53] memoise_1.1.0                 gridExtra_2.3                
[55] stringi_1.5.3                 RSQLite_2.2.1                
[57] BiocVersion_3.10.1            desc_1.2.0                   
[59] pkgbuild_1.1.0                BiocParallel_1.20.1          
[61] rlang_0.4.9                   pkgconfig_2.0.3              
[63] matrixStats_0.57.0            bitops_1.0-6                 
[65] lattice_0.20-38               GenomicAlignments_1.22.1     
[67] processx_3.4.5                bit_4.0.4                    
[69] tidyselect_1.1.0              plyr_1.8.6                   
[71] magrittr_2.0.1                R6_2.5.0                     
[73] generics_0.1.0                DelayedArray_0.12.3          
[75] DBI_1.1.0                     withr_2.3.0                  
[77] pillar_1.4.7                  haven_2.3.1                  
[79] RCurl_1.98-1.2                modelr_0.1.8                 
[81] crayon_1.3.4                  usethis_1.6.3                
[83] progress_1.2.2                grid_3.6.2                   
[85] readxl_1.3.1                  callr_3.5.1                  
[87] blob_1.2.1                    reprex_0.3.0                 
[89] digest_0.6.27                 xtable_1.8-4                 
[91] httpuv_1.5.4                  openssl_1.4.3                
[93] munsell_0.5.0                 sessioninfo_1.1.1            
[95] askpass_1.1

Thank you in advance for your help,

Best, Antara

ErrorinUseMethod("filter_") biomaRt • 3.0k views
ADD COMMENT
0
Entering edit mode
@martin-morgan-1513
Last seen 10 weeks ago
United States

Hello antara!

Posts similar to yours can already be found at:

We encourage you to look at the sources listed above for more answers.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

PS: ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tbl_dbi', 'tbl_sql', 'tbl_lazy', 'tbl')"

ADD COMMENT
0
Entering edit mode

Hi antara,

Did this method Martin suggested work for you? I'm also using honey badger getting a similar error but the solution still does not work for me.

Thanks you!

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